src/hg/makeDb/trackDb/trackDb.ra 1.547
1.547 2009/12/07 22:00:39 hiram
Move all the chainNet definitions off to their own file
Index: src/hg/makeDb/trackDb/trackDb.ra
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/trackDb.ra,v
retrieving revision 1.546
retrieving revision 1.547
diff -b -B -U 4 -r1.546 -r1.547
--- src/hg/makeDb/trackDb/trackDb.ra 7 Dec 2009 17:42:39 -0000 1.546
+++ src/hg/makeDb/trackDb/trackDb.ra 7 Dec 2009 22:00:39 -0000 1.547
@@ -1,4 +1,6 @@
+include trackDb.chainNet.ra
+
# Root trackDb.ra file. Files from the organism subdirectory and the database sub-sub directory
# will be layered on. Organism is something like 'human' and database is something
# like 'hg18'. See the README file in this directory for a description of the format.
#
@@ -2056,51 +2058,8 @@
spectrum on
type netAlign fr1 chainFr1
otherDb fr1
-# release alpha until individual fr2 tracks are obsolete
-track chainNetFr2
-release alpha
-compositeTrack on
-shortLabel Fugu Chain/Net
-longLabel Fugu (Oct. 2004/fr2), Chain and Net Alignments
-subGroup1 view Views chain=Chain net=Net
-dragAndDrop subTracks
-visibility hide
-visibilityViewDefaults chain=pack net=dense
-group compGeno
-noInherit on
-priority 159
-color 0,0,0
-altColor 255,255,0
-type bed 3
-settingsByView chain:spectrum=on
-sortOrder view=+
-matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
-matrixHeader A, C, G, T
-otherDb fr2
-chainMinScore 5000
-chainLinearGap loose
-spectrum on
-html chainNet
-
- track chainFr2
- release alpha
- subTrack chainNetFr2
- subGroups view=chain
- shortLabel $o_Organism Chain
- longLabel $o_Organism ($o_date/$o_db) Chained Alignments
- type chain fr2
-
- track netFr2
- release alpha
- subTrack chainNetFr2
- subGroups view=net
- shortLabel $o_Organism Net
- longLabel $o_Organism ($o_date/$o_db) Alignment Net
- type netAlign fr2 chainFr2
-
-
# release beta until composite chainNetFr2 track becomes the default
track chainFr2
release beta
shortLabel $o_Organism Chain
@@ -2127,46 +2086,8 @@
spectrum on
type netAlign fr2 chainFr2
otherDb fr2
-track chainNetTetNig2
-compositeTrack on
-shortLabel Tetraodon Chain/Net
-longLabel Tetraodon (Mar. 2007/tetNig2), Chain and Net Alignments
-subGroup1 view Views chain=Chain net=Net
-dragAndDrop subTracks
-visibility hide
-visibilityViewDefaults chain=pack net=dense
-group compGeno
-noInherit on
-priority 159
-color 0,0,0
-altColor 255,255,0
-type bed 3
-settingsByView chain:spectrum=on
-sortOrder view=+
-matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
-matrixHeader A, C, G, T
-otherDb tetNig2
-chainMinScore 5000
-chainLinearGap loose
-spectrum on
-html chainNet
-
- track chainTetNig2
- subTrack chainNetTetNig2
- subGroups view=chain
- shortLabel $o_Organism Chain
- longLabel $o_Organism ($o_date/$o_db) Chained Alignments
- type chain tetNig2
-
- track netTetNig2
- subTrack chainNetTetNig2
- subGroups view=net
- shortLabel $o_Organism Net
- longLabel $o_Organism ($o_date/$o_db) Alignment Net
- type netAlign tetNig2 chainTetNig2
-
track chainTetNig1
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
group compGeno
@@ -2187,46 +2108,8 @@
spectrum on
type netAlign tetNig1 chainTetNig1
otherDb tetNig1
-track chainNetDanRer6
-compositeTrack on
-shortLabel Zebrafish Chain/Net
-longLabel Zebrafish (Dec. 2008/danRer6), Chain and Net Alignments
-subGroup1 view Views chain=Chain net=Net
-dragAndDrop subTracks
-visibility hide
-visibilityViewDefaults chain=pack net=dense
-group compGeno
-noInherit on
-priority 159
-color 0,0,0
-altColor 255,255,0
-type bed 3
-settingsByView chain:spectrum=on
-sortOrder view=+
-matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
-matrixHeader A, C, G, T
-otherDb danRer6
-chainMinScore 5000
-chainLinearGap loose
-spectrum on
-html chainNet
-
- track chainDanRer6
- subTrack chainNetDanRer6
- subGroups view=chain
- shortLabel $o_Organism Chain
- longLabel $o_Organism ($o_date/$o_db) Chained Alignments
- type chain danRer6
-
- track netDanRer6
- subTrack chainNetDanRer6
- subGroups view=net
- shortLabel $o_Organism Net
- longLabel $o_Organism ($o_date/$o_db) Alignment Net
- type netAlign danRer6 chainDanRer6
-
track chainDanRer5
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
group compGeno
@@ -2355,51 +2238,8 @@
spectrum on
type netAlign petMar1 chainPetMar1
otherDb petMar1
-# release alpha until individual oryLat2 tracks are obsolete
-track chainNetOryLat2
-release alpha
-compositeTrack on
-shortLabel Medaka Chain/Net
-longLabel Medaka (Oct. 2005/oryLat2), Chain and Net Alignments
-subGroup1 view Views chain=Chain net=Net
-dragAndDrop subTracks
-visibility hide
-visibilityViewDefaults chain=pack net=dense
-group compGeno
-noInherit on
-priority 165.5
-color 100,50,0
-altColor 255,240,200
-type bed 3
-settingsByView chain:spectrum=on
-sortOrder view=+
-matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
-matrixHeader A, C, G, T
-otherDb hg19
-chainMinScore 3000
-chainLinearGap medium
-html chainNet
-
- track chainOryLat2
- release alpha
- subTrack chainNetOryLat2
- subGroups view=chain
- shortLabel $o_Organism Chain
- longLabel $o_Organism ($o_date/$o_db) Chained Alignments
- type chain oryLat2
- otherDb oryLat2
-
- track netOryLat2
- release alpha
- subTrack chainNetOryLat2
- subGroups view=net
- shortLabel $o_Organism Net
- longLabel $o_Organism ($o_date/$o_db) Alignment Net
- type netAlign oryLat2 chainOryLat2
- otherDb oryLat2
-
# release beta until composite oryLat2 tracks become the default
track chainOryLat2
release beta
shortLabel $o_Organism Chain
@@ -2450,50 +2290,8 @@
spectrum on
type netAlign oryLat1 chainOryLat1
otherDb oryLat1
-# release alpha until individual gasAcu1 tracks are obsolete
-track chainNetGasAcu1
-compositeTrack on
-shortLabel Stickleback Chain/Net
-longLabel Stickleback (Feb 2006/gasAcu1), Chain and Net Alignments
-subGroup1 view Views chain=Chain net=Net
-dragAndDrop subTracks
-visibility hide
-visibilityViewDefaults chain=pack net=dense
-group compGeno
-noInherit on
-priority 181
-color 0,0,0
-altColor 255,255,0
-type bed 3
-settingsByView chain:spectrum=on
-sortOrder view=+
-matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
-matrixHeader A, C, G, T
-otherDb gasAcu1
-chainMinScore 3000
-chainLinearGap medium
-spectrum on
-html chainNet
-release alpha
-
- track chainGasAcu1
- release alpha
- subTrack chainNetGasAcu1
- subGroups view=chain
- shortLabel $o_Organism Chain
- longLabel $o_Organism ($o_date/$o_db) Chained Alignments
- type chain gasAcu1
-
- track netGasAcu1
- release alpha
- subTrack chainNetGasAcu1
- subGroups view=net
- shortLabel $o_Organism Net
- longLabel $o_Organism ($o_date/$o_db) Alignment Net
- type netAlign gasAcu1 chainGasAcu1
-
# release beta until composite gasAcu1 tracks become the default
track chainGasAcu1
release beta
shortLabel $o_Organism Chain
@@ -2615,50 +2413,8 @@
spectrum on
type netAlign galGal2 chainGalGal2
otherDb galGal2
-# release alpha until individual galGal3 tracks are obsolete
-track chainNetGalGal3
-compositeTrack on
-shortLabel Chicken Chain/Net
-longLabel Chicken (May 2006/galGal3), Chain and Net Alignments
-subGroup1 view Views chain=Chain net=Net
-dragAndDrop subTracks
-visibility hide
-visibilityViewDefaults chain=pack net=dense
-group compGeno
-noInherit on
-priority 181
-color 0,0,0
-altColor 255,255,0
-type bed 3
-settingsByView chain:spectrum=on
-sortOrder view=+
-matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
-matrixHeader A, C, G, T
-otherDb galGal3
-chainMinScore 3000
-chainLinearGap medium
-spectrum on
-html chainNet
-release alpha
-
- track chainGalGal3
- release alpha
- subTrack chainNetGalGal3
- subGroups view=chain
- shortLabel $o_Organism Chain
- longLabel $o_Organism ($o_date/$o_db) Chained Alignments
- type chain galGal3
-
- track netGalGal3
- release alpha
- subTrack chainNetGalGal3
- subGroups view=net
- shortLabel $o_Organism Net
- longLabel $o_Organism ($o_date/$o_db) Alignment Net
- type netAlign galGal3 chainGalGal3
-
track chainGalGal3
release beta
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
@@ -2739,50 +2495,8 @@
type netAlign taeGut1 chainTaeGut1
otherDb taeGut1
release beta
-# release alpha until ornAna1 individual chain/net tracks phased out
-track chainNetOrnAna1
-compositeTrack on
-shortLabel Platypus Chain/Net
-longLabel Platypus (Mar. 2007/ornAna1), Chain and Net Alignments
-subGroup1 view Views chain=Chain net=Net
-dragAndDrop subTracks
-visibility hide
-visibilityViewDefaults chain=pack net=dense
-group compGeno
-noInherit on
-priority 191
-color 0,0,0
-altColor 255,255,0
-type bed 3
-settingsByView chain:spectrum=on
-sortOrder view=+
-matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
-matrixHeader A, C, G, T
-otherDb ornAna1
-chainMinScore 3000
-chainLinearGap medium
-spectrum on
-html chainNet
-release alpha
-
- track chainOrnAna1
- release alpha
- subTrack chainNetOrnAna1
- subGroups view=chain
- shortLabel $o_Organism Chain
- longLabel $o_Organism ($o_date/$o_db) Chained Alignments
- type chain ornAna1
-
- track netOrnAna1
- release alpha
- subTrack chainNetOrnAna1
- subGroups view=net
- shortLabel $o_Organism Net
- longLabel $o_Organism ($o_date/$o_db) Alignment Net
- type netAlign ornAna1 chainOrnAna1
-
# release beta until ornAna1 individual chain/net tracks phased out
track chainOrnAna1
release beta
shortLabel $o_Organism Chain
@@ -2833,46 +2547,8 @@
spectrum on
type netAlign macEug1 chainMacEug1
otherDb macEug1
-track chainNetMonDom5
-compositeTrack on
-shortLabel Opossum Chain/Net
-longLabel Opossum (Oct. 2006/monDom5), Chain and Net Alignments
-subGroup1 view Views chain=Chain net=Net
-dragAndDrop subTracks
-visibility hide
-visibilityViewDefaults chain=pack net=dense
-group compGeno
-noInherit on
-priority 191
-color 0,0,0
-altColor 255,255,0
-type bed 3
-settingsByView chain:spectrum=on
-sortOrder view=+
-matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
-matrixHeader A, C, G, T
-otherDb monDom5
-chainMinScore 3000
-chainLinearGap medium
-spectrum on
-html chainNet
-
- track chainMonDom5
- subTrack chainNetMonDom5
- subGroups view=chain
- shortLabel $o_Organism Chain
- longLabel $o_Organism ($o_date/$o_db) Chained Alignments
- type chain monDom5
-
- track netMonDom5
- subTrack chainNetMonDom5
- subGroups view=net
- shortLabel $o_Organism Net
- longLabel $o_Organism ($o_date/$o_db) Alignment Net
- type netAlign monDom5 chainMonDom5
-
track chainMonDom4
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
group compGeno
@@ -3075,50 +2751,8 @@
spectrum on
type netAlign mm6 chainMm6
otherDb mm6
-# release alpha until mm9 individual chain/net tracks phased out
-track chainNetMm9
-compositeTrack on
-shortLabel Mouse Chain/Net
-longLabel Mouse (Jul. 2007/mm9), Chain and Net Alignments
-subGroup1 view Views chain=Chain net=Net
-dragAndDrop subTracks
-visibility hide
-visibilityViewDefaults chain=pack net=dense
-group compGeno
-noInherit on
-priority 209
-color 0,0,0
-altColor 255,255,0
-type bed 3
-settingsByView chain:spectrum=on
-sortOrder view=+
-matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
-matrixHeader A, C, G, T
-otherDb mm9
-chainMinScore 3000
-chainLinearGap medium
-spectrum on
-html chainNet
-release alpha
-
- track chainMm9
- release alpha
- subTrack chainNetMm9
- subGroups view=chain
- shortLabel $o_Organism Chain
- longLabel $o_Organism ($o_date/$o_db) Chained Alignments
- type chain mm9
-
- track netMm9
- release alpha
- subTrack chainNetMm9
- subGroups view=net
- shortLabel $o_Organism Net
- longLabel $o_Organism ($o_date/$o_db) Alignment Net
- type netAlign mm9 chainMm9
-
track chainMm9
release beta
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
@@ -3361,88 +2995,8 @@
spectrum on
type netAlign bosTau1 chainBosTau1
otherDb bosTau1
-track chainNetEquCab2
-compositeTrack on
-shortLabel Horse Chain/Net
-longLabel Horse (Sep. 2007/equCab2), Chain and Net Alignments
-subGroup1 view Views chain=Chain net=Net
-dragAndDrop subTracks
-visibility hide
-visibilityViewDefaults chain=pack net=dense
-group compGeno
-noInherit on
-priority 240
-color 0,0,0
-altColor 255,255,0
-type bed 3
-settingsByView chain:spectrum=on
-sortOrder view=+
-matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
-matrixHeader A, C, G, T
-otherDb equCab2
-chainMinScore 3000
-chainLinearGap medium
-spectrum on
-html chainNet
-
- track chainEquCab2
- subTrack chainNetEquCab2
- subGroups view=chain
- shortLabel $o_Organism Chain
- longLabel $o_Organism ($o_date/$o_db) Chained Alignments
- type chain equCab2
-
- track netEquCab2
- subTrack chainNetEquCab2
- subGroups view=net
- shortLabel $o_Organism Net
- longLabel $o_Organism ($o_date/$o_db) Alignment Net
- type netAlign equCab2 chainEquCab2
-
-# release alpha until canFam2 individual tracks phased out
-track chainNetCanFam2
-compositeTrack on
-shortLabel Dog Chain/Net
-longLabel Dog (May 2005/canFam2), Chain and Net Alignments
-subGroup1 view Views chain=Chain net=Net
-dragAndDrop subTracks
-visibility hide
-visibilityViewDefaults chain=pack net=dense
-group compGeno
-noInherit on
-priority 240
-color 0,0,0
-altColor 255,255,0
-type bed 3
-settingsByView chain:spectrum=on
-sortOrder view=+
-matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
-matrixHeader A, C, G, T
-otherDb canFam2
-chainMinScore 3000
-chainLinearGap medium
-spectrum on
-html chainNet
-release alpha
-
- track chainCanFam2
- release alpha
- subTrack chainNetCanFam2
- subGroups view=chain
- shortLabel $o_Organism Chain
- longLabel $o_Organism ($o_date/$o_db) Chained Alignments
- type chain canFam2
-
- track netCanFam2
- release alpha
- subTrack chainNetCanFam2
- subGroups view=net
- shortLabel $o_Organism Net
- longLabel $o_Organism ($o_date/$o_db) Alignment Net
- type netAlign canFam2 chainCanFam2
-
track chainCanFam2
release beta
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
@@ -4789,115 +4343,4 @@
searchTable ccdsGene
searchType genePred
searchPriority 1.1
-
-track chainNetVenter
-compositeTrack on
-shortLabel Venter Chain/Net
-longLabel J. Craig Venter Chain and Net Alignments
-subGroup1 view Views chain=Chains net=Nets
-dragAndDrop subTracks
-visibility hide
-visibilityViewDefaults chain=pack net=dense
-group compGeno
-noInherit on
-priority 500
-color 0,0,0
-altColor 255,255,0
-type bed 3
-settingsByView chain:spectrum=on
-sortOrder view=+
-
- track chainVenter1
- subTrack chainNetVenter off
- subGroups view=chain
- shortLabel $o_Organism Chain
- longLabel $o_Organism ($o_date/$o_db) Chained Alignments
- color 100,50,0
- altColor 255,240,200
- matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
- matrixHeader A, C, G, T
- type chain venter1
- otherDb venter1
-
- track netVenter1
- subTrack chainNetVenter off
- subGroups view=net
- shortLabel $o_Organism Net
- longLabel $o_Organism ($o_date/$o_db) Alignment Net
- type netAlign venter1 chainVenter1
- otherDb venter1
-
-track chainNetHg19
-compositeTrack on
-shortLabel Human Chain/Net
-longLabel Human (Feb. 2009/hg19), Chain and Net Alignments
-subGroup1 view Views chain=Chain net=Net
-dragAndDrop subTracks
-visibility hide
-visibilityViewDefaults chain=pack net=dense
-group compGeno
-noInherit on
-priority 498
-color 0,0,0
-altColor 255,255,0
-type bed 3
-settingsByView chain:spectrum=on
-sortOrder view=+
-matrix 16 90,-330,-236,-356,-330,100,-318,-236,-236,-318,100,-330,-356,-236,-330,90
-matrixHeader A, C, G, T
-otherDb hg19
-chainMinScore 3000
-chainLinearGap medium
-html chainNet
-
- track chainHg19
- subTrack chainNetHg19
- subGroups view=chain
- shortLabel $o_Organism Chain
- longLabel $o_Organism ($o_date/$o_db) Chained Alignments
- type chain hg19
-
- track netHg19
- subTrack chainNetHg19
- subGroups view=net
- shortLabel $o_Organism Net
- longLabel $o_Organism ($o_date/$o_db) Alignment net
- type netAlign hg19 chainHg19
-
-track chainNetPoodle
-compositeTrack on
-shortLabel Poodle Chain/Net
-longLabel Poodle Chain and Net Alignments
-subGroup1 view Views chain=Chains net=Nets
-dragAndDrop subTracks
-visibility hide
-visibilityViewDefaults chain=pack net=dense
-group compGeno
-noInherit on
-priority 500
-color 0,0,0
-altColor 255,255,0
-type bed 3
-settingsByView chain:spectrum=on
-sortOrder view=+
-
- track chainCanFamPoodle1
- subTrack chainNetPoodle off
- subGroups view=chain
- shortLabel $o_Organism Chain
- longLabel $o_Organism ($o_date/$o_db) Chained Alignments
- color 100,50,0
- altColor 255,240,200
- matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
- matrixHeader A, C, G, T
- type chain canFamPoodle1
- otherDb canFamPoodle1
-
- track netCanFamPoodle1
- subTrack chainNetPoodle off
- subGroups view=net
- shortLabel $o_Organism Net
- longLabel $o_Organism ($o_date/$o_db) Alignment Net
- type netAlign canFamPoodle1 chainCanFamPoodle1
- otherDb canFamPoodle1